In the episode "Toy Scary Boo", they try something different and have Fred and Shaggy pair up when it's time to split up. It gets awkward.
Fred: So... did you see the game last night?
Shaggy: Uh, I'm not really into sports.
Fred: Oh, right...
Shaggy: Wanna go get something to eat?
Fred: No thanks, I'm not hungry.
Fred: From now on let's split up like we normally do.
In "Homeward Hound", the cat creature is chasing Velma, who runs to the Mystery Machine and pulls out a ball of yarn to distract it. It works.
In "It's All Greek to Scooby", Velma sputtering in frustration at not being able to correctly deduce the identity of the culprit as it was someone she had never seen before. She even angrily declares that "this one doesn't count", since there was no way she would have been able to solve the mystery.
From "A Terrifying Round With A Menacing Metallic Clown," Velma goes cowering off with Scooby (she's got a clown phobia) to the pitching cages. As she's bracing for a pitch from Scooby, she gets a slice of pizza from the pitching machine Scooby is operating. She never realized cowering off could be so much fun.
Her turning down a Scooby Snack is also hilarious:
Velma: Nice try, Daphne; I may be scared, but I'm not desperate.
In "The Vampire Strikes Back", Shaggy and Scooby believe Fred has been turned into a bat by the vampire. They finally caught it until they found Fred. Realizing the bat is really a bat, Shaggy and Scooby ran away, with the bat flying after them, apparently taking a liking to them.
In "Riva Ras Regas", Del Stone gives them a tour through the Newark Newark Casino. When he jokes that he chose the Newark theme because there's already a casino using a pirate theme, Fred thinks it's the real reason and says it makes sense. Stone later explains the reason behind Speckle Hall and Fred mistakes it for a funny joke until Stone explains it's not a joke.